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Fox is a research head and friend of Thomas Wayne who is demoted by Wayne Enterprises CEO William Earle to overseeing the supplies of Wayne Enterprises' aborted research projects and prototypes. Upon returning to the business, Bruce Wayne strikes up a fast friendship which allows him to all but recruit Fox as his armorer for his Batman activities. Fox proves invaluable in this role, even when he is fired by Earle. Among other things, he supplies Wayne with the materials that will eventually become the Batsuit and the Batmobile. In addition, Fox provides the cure for the Scarecrow's fear toxin.

Regarding Wayne's identity as Batman, he tells Wayne "If you don't want to tell me exactly what you're doing, when I'm asked, I don't have to lie. But don't think of me as an idiot." At the end of the film, Wayne, having gained majority control of Wayne Enterprises' shares, makes Fox the company's CEO.

In The Dark Knight, Fox is obviously aware that Bruce Wayne is Batman- at one point conversing with Wayne in the Batsuit- and actively participates in a support capacity as Wayne's armorer, providing him with additional equipment such as the Batpod and a new Batsuit designed for more efficient mobility. In addition, Fox participates in his employer's vigilante activities both in the Batcave and in the field as his technical assistant and reconnaissance expert, using his professional duties as cover. Fox eventually learns that Wayne has expanded on the sonar technology and developed an advanced surveillance system that can listen in and track the movement of any of the thousands of cell phones in the city, but to ensure that the system is not misused Bruce has designed it so that only Fox can control it. Since this essentially contradicts everything Wayne believes in, Fox agrees to help but says he will resign if the machine is not destroyed after the Joker is gone. After the Joker is apprehended, Fox enters a code (his own name) as instructed by Wayne, which activates a self-destruct function for the system, and Fox continues to work under Wayne.

Lucius Fox is surprised to hear of Bruce's emergence from hiding and offers to take him on a guided tour of the Applied Sciences Division, revealing the new vehicle The Bat, possibly dropping a hint to Bruce that Batman may still be needed.

After Bruce loses his fortune and seat on the board of directors of Wayne Enterprises, Miranda Tate (Talia al Ghul) becomes the new CEO and chair of the board, replacing Lucius. Lucius' role becomes that of company president.

Following Bane's takeover of Gotham City, Fox is coerced into unlocking the Wayne Enterprises nuclear fusion reactor with his fingerprints by Bane who was holding fellow board member Douglas Fredericks gunpoint, thereby enabling kidnapped nuclear physist Dr. Leonid Pavel to prime the reactor and turn it into a functioning weapon. Fox later attempts to deactivate the nuclear reactor but Talia activates the flooding mechanism and he is forced to leave the chamber. After Bruce Wayne's "death", Lucius attends his funeral service alongside Alfred, Jim Gordon and John Blake. Sometime later, he learned about the software patch that Bruce Wayne used to fix the auto pilot problem on The Bat. Fox is once again head of Wayne Enterprises and has begun the process of rebuilding it back in a thriving company.